The 22-year-old earned an estimated $34.5 million from May 2011 to May 2012 and pushed Angelina Jolie into fourth place.
Cameron Diaz, who had a surprise hit with "Bad Teacher", came in second with $34 million.
"She (Stewart) is an up-and-coming star. She is earning a lot of money from one of the most successful franchises of all time. This is who you would expect to see right now," said Dorothy Pomerantz, Forbes Los Angeles bureau chief.
"This year you are seeing somebody young and at the brink of potentially great stardom sitting on the top of the list."
Forbes.com compiled the list and estimated salaries by talking to agents, managers and lawyers and based earnings on pay, profits, residuals, endorsements and advertising work.
Oscar-winner Sandra Bullock, who largely took a break from filming after 2009's "The Blind Side", came third with $25 million.
Jolie, who topped last year's list along with Sarah Jessica Parker, dropped to the fourth spot with earnings of $20 million while Charlize Theron, Stewart's co-star in "Snow White and the Huntsman" who also appears in "Prometheus", trailed at $18 million, and rounded out the top five places.
Parker, whose 2011 film "I Don't Know How She Does It" brought in a disappointing $30 million at the worldwide box office, slipped to seventh place with a $15 million salary.
"She is almost earning more from her perfume and endorsement deals right now than from entertainment. That is true of a lot of women. They have these outside deals that are very lucrative. Angelina Jolie earns a lot from residuals, as does Sarah Jessica Parker," Pomerantz said.
Former "Friends" star Jennifer Anniston just made the list, earning an $11 million salary.
The top 10 actresses earned a total of $200 million, according to Forbes.com, a lot less than the $361 million total that the 10 highest-earning men made.
"It is nowhere near what men are making," Pomerantz said. "I think it will be a while until women see salary parity, if it ever happens. Women are paid less in every industry, not just in Hollywood."
The full list can be found here
(Reporting by Patricia Reaney; Editing by Jill Serjeant and Dale Hudson)
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